When we think of cross-linked peptides, we traditionally think of them as something that occurs pairwise:
"peptide A has crosslinked to peptide B".
But be a little generous when pouring in your cross-linking reagent, and you will find that your protein forms so many cross-links that you can
easily have more that two peptides in the same precursor, following digest.
MassAI now comes with an optional feature, which identifies double cross-links. This is obviously time consuming if you carry out a free-for-
all cross-link search, but you can cut down significantly on the search time by ticking the checkbox "Cross-link peptide ONLY if peptide has
been observed" (see below).